Carno, you are correct that I wasn't prepared for OCS, and obviously scoring 100's on the crunch/pullup portion doesn't mean much as it relates to running.
Running for me has always been a weakness, so I make the mistake in assuming that as long as I made passing PFT scores that I could compensate for that weak point with crunches, pullups, or whatever else I could that wasn't running. Big mistake. Do not do this. I'm trying to point this out so others don't end up where I am.
And, what USMCEcho4 says is dead on. They know which event you're likely to be marginal at, and you will get attention for it, and possibly chits. You don't want a stack of those. Being is the middle is where you want to be, run-wise, if you're fast enough to be able to "game the game," as it were.
As far as the stress fractures go, they are another thing entirely, which is best covered else where, but be sure you train properly. This means push hard, but be sure your technique for running is sound and you don't overtrain so much before you go that you're prone to breaking while you're there. I went from couch potato, basically, to trying to run 3-5 miles as hard as I could. You can do this, and your muscles and cardio will grow strong enough to do compensate fairly quickly. But, your bones will not. They need time to lay down tissue, so start easy and increase distance incrementally.
Oh, Cunningham, my pre-ship was around 23 minutes, I think. Sure, that's passing, but you need better than that to do well. Your initial PFT will suck because you're tired, getting used to the new environment, and whatever other reasons you can think of. Your score is likely to drop across the board, especially your run. Mine came in at 23:40, so they pegged me right away. Don't be that guy. There are plenty of other things to worry about than, "I don't want to fall out on the next run," which is pretty much every other day at least.
I've heard of people not pushing hard on the initial PFT, as a "game the game" strategy. The idea is to show a marginal score initially so that it's easier to demonstrate improvement on later events. I wouldn't advise doing this. Put out on your initial, if for no other reason that what I said above. You won't be performing as well as you expect to, and you don't want to run the risk of a marginal score, or, worse a failing one. If you come in under 23:45 (which I cleared by a mere 5 seconds,) you have to re-run it the next day. Failing that, you go home. Again, you'll have lots of things to be concerned with, and you don't want to fret over something this crucial.
Sorry if this sounds like a rant, but I really don't want other candidates to get jacked up as I did. There's a lot at stake.